Welcome to the GPCRdb documentation

The GPCRdb contains data, diagrams and web tools for G protein-coupled receptors (GPCRs). Users can browse all GPCR crystal structures and the largest collection of receptor mutants. Diagrams can be produced and downloaded to illustrate receptor residues (snake-plot and helix box diagrams) and relationships (phylogenetic trees). Reference (crystal) structure-based sequence alignments take into account helix bulges and constrictions, display statistics of amino acid conservation and have been assigned generic residue numbering for equivalent residues in different receptors.

The source code and source data are freely available on GitHub.

Below, a table overview of all the different pages and functionalities in GPCRdb grouped by sections, along links to specific documentation pages, associated slides and video demonstrations.

Below, a table overview of all the different pages and functionalities in GPCRdb grouped by sections, along links to specific documentation pages, associated slides and video demonstrations.

SEQUENCES
Page name Video Slides Demo Reference Short description
Sequence alignments
Sequence alignment Video Isberg et al. NAR 2016
Kooistra et al. NAR 2021
Provides sequence alignments analyses of receptors.
Generic residue number tables
Isberg et al. TiPS 2015 Displays the generic residue number tables
for the single or set of receptors selected.
Genetic variants
Hauser et al. Cell 2018 Section showing the variation coverage,
single receptor variants and the estimated
economic burden for drugs targeting GPCRs
Isoforms
Marti-Solano et al. Nature 2020 Info page highlighting the number
of unique isoforms detected for
each receptor gene
STRUCTURES
Page name Video Slides Demo Reference Short description
Structure coverage
Structure coverage Video Isberg et al. NAR 2016 Overview of the structure information
available in GPCRdb. Data is shown using
detailed inforgraphics and plots.
Structures
Structures Video Isberg et al. NAR 2014
Kooistra et al. NAR 2021
Browser page listing detailed information
for all the structures present in GPCRdb.
Structure models
Structure models Video Pándy-Szekeres et al. NAR 2023 Browser page listing all the AlphaFold
generated homology models present in GPCRdb,
with their original associate template.
Structure model validation
Structure model validation Video Kooistra et al. NAR 2021
Pándy-Szekeres et al. NAR 2023
Browser page listing the RMSD values
comparing the latest model before a structure of the
same receptor in the same state was published.
STRUCTURE ANALYSIS
Page name Video Slides Demo Reference Short description
Structure comparison tool
Structure comparison tool Video Kooistra et al. Nat. Struct. Mol. Biol 2021 Interactive tool for investigation of single structures
or comparison of sets of structures. The tool allow
for more than 20 different plot representations
and lists available contact position pairs.
Structure similarity trees
Structure similarity trees Video Kooistra et al. Nat. Struct. Mol. Biol 2021 Interactive tool showcasing the similarity trees
of selected set of receptors. Generated trees can be
further graphically tweaked and downloaded
in high resolution format.
Structure superposition
Isberg et al. NAR 2016 Functionality designed for the superimposition of user
defined structures (reference and test), allowing
analysis for full structures or segment based.
Generic residue numbering (PDB)
Isberg et al. NAR 2016
Isberg et al. TiPS 2015
Functionality for the annotation using generic numbers
from GPCRdb of user uploaded PDB files.
STRUCTURE CONSTRUCTS
Page name Video Slides Demo Reference Short description
Construct/Experiment design
Munk et al. Nat. Methods 2019 Section for the design and alignment of experimental constructs,
and associated browser page listing experiments walkthrough.
Truncation/Fusion analysis
Munk et al. Nat. Methods 2019 Section with pages showing information about truncation sites,
fusion sites and deletion loops across the available GPCRdb data.
Mutation analysis
Munk et al. Nat. Methods 2019 Section with mutations oriented browsers,
listing stabilizing mutations, substitution matrix
and a dedicated stabilising mutation analyser.
LIGANDS & BIOACTIVITIES
Page name Video Slides Demo Reference Short description
Ligand coverage
Ligand coverage Video Pándy-Szekeres et al. NAR 2018 Overview of the ligands information available in GPCRdb.
Data is shown using detailed inforgraphics and plots.
Ligands (ChEMBL, GtP, Ki db)
Ligand search Video Pándy-Szekeres et al. NAR 2018
Pándy-Szekeres et al. NAR 2023
Section allowing the search for ligands associated
to a specific receptor or using ligand name, database ID
or chemical information (SMILES or Inchikey).
DRUGS & AGENTS IN TRIAL
Page name Video Slides Demo Reference Short description
Drugs targets and indicators
Hauser et al. Nat. Rev. Drug Discov 2017 Browser page listing information about drugs,
their targets of action, therapeutic indication and
clinical status, with associated references.
Drug target tree
Hauser et al. Nat. Rev. Drug Discov 2017 Interactive infographic tree showing drug data
information on established or under clinical trials
GPCR targets.
Drug statistics
Hauser et al. Nat. Rev. Drug Discov 2017 Overview of the GPCR class as drug target,
with focus on receptor family targets, drug molecule types,
mode of action and disease indications.
LIGAND SITES
Page name Video Slides Demo Reference Short description
GPCR-ligand interactions
Isberg et al. NAR 2016
Munk et al. COPHAR 2016
Functionality showing the protein-ligand interactions
for the available PDB structures in GPCRdb using graphical
representation and 3D visualization tools.
Site search
Isberg et al. NAR 2016 Section designed for the investigation of protein-ligand
interactions of set of receptors, either using sequence motifs
or ligand complex though a user defined PDB file.
LIGAND SITE MUTATIONS
Page name Video Slides Demo Reference Short description
Mutation coverage
Munk et al. COPHAR 2016 Overview of the mutations information available in GPCRdb.
Data is shown using detailed inforgraphics.
Mutations
Mutations Video Munk et al. COPHAR 2016 Browser page listing mutations for user selected receptors
and protein segments. Result tables also provides information about
ligand affinity for the mutation (FoldChange) if available.
Mutation design tool
Munk et al. COPHAR 2016 Section with mutation design tool based either
on a PDB code or receptor name. Result page lists suggested mutations
with associated structure interactions, supporting ligands,
receptors and mutagenesis experiments.
Mutation data submission
Munk et al. COPHAR 2016 Description to the mutation data submission form
and guidelines on how to submit your experimental data to GPCRdb.

The documentation is organised into three sections: